2024-05-14 |
Ben Soares | JAL-4414 Add a FileNotFoundException when identifying... |
blob | commitdiff |
2024-01-23 |
James Procter | Merge branch 'develop' into bug/JAL-4290_headless_align... |
blob | commitdiff | diff to current |
2024-01-23 |
James Procter | JAL-4369 invokeAndWait to avoid hang whilst calling... |
blob | commitdiff | diff to current |
2024-01-05 |
Ben Soares | JAL-4368 Only set a colour scheme if --colour is given... bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately |
blob | commitdiff | diff to current |
2023-12-18 |
Ben Soares | JAL-4290 incorrect usage of main() |
blob | commitdiff | diff to current |
2023-12-15 |
Ben Soares | JAL-4290 Add method to allow for specific settings... |
blob | commitdiff | diff to current |
2023-12-15 |
Ben Soares | JAL-4290 Set structureSelectionManager settings more... |
blob | commitdiff | diff to current |
2023-12-15 |
Ben Soares | JAL-4290 Move some annotation visibility settings to... |
blob | commitdiff | diff to current |
2023-12-05 |
Ben Soares | JAL-4353 Add secondary Types for Args, for STRUCTUREIMA... |
blob | commitdiff | diff to current |
2023-11-13 |
James Procter | JAL-4090 JAL-1551 source license |
blob | commitdiff | diff to current |
2023-11-02 |
James Procter | JAL-4217 wrap progress bar creation in an invokeLater... |
blob | commitdiff | diff to current |
2023-10-25 |
James Procter | JAL-4312 call AlignFrame.setAnnotationsVisibility on... |
blob | commitdiff | diff to current |
2023-10-20 |
Ben Soares | JAL-4298 Remove a stray return in the processGroovyScri... |
blob | commitdiff | diff to current |
2023-10-18 |
Ben Soares | JAL-629 Run non-alignframe linked groovy scripts. ... |
blob | commitdiff | diff to current |
2023-09-29 |
James Procter | JAL-629 JAL-4265 JAL-4286 report the filename for the... |
blob | commitdiff | diff to current |
2023-09-21 |
Ben Soares | JAL-4265 Use ColourUtils.parseColourString() for consis... merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285 |
blob | commitdiff | diff to current |
2023-09-20 |
James Procter | JAL-4285 don’t say you are reporting warnings/errors... |
blob | commitdiff | diff to current |
2023-09-20 |
James Procter | JAL-4265 JAL-4286 reinstated explicit restoreSession... |
blob | commitdiff | diff to current |
2023-09-20 |
James Procter | JAL-4265 bail early when attempting to export a view... |
blob | commitdiff | diff to current |
2023-09-19 |
Ben Soares | JAL-4265 Change to use JmolCommands |
blob | commitdiff | diff to current |
2023-09-19 |
Ben Soares | JAL-629 Allow multiple structure images for multiple... |
blob | commitdiff | diff to current |
2023-09-16 |
Ben Soares | JAL-629 Fix a test and omit an incorrect error message... improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters |
blob | commitdiff | diff to current |
2023-09-16 |
Ben Soares | JAL-4265 Added --bgcolour for --structureimage output... |
blob | commitdiff | diff to current |
2023-09-16 |
Ben Soares | JAL-4269 Now using --width, --height, --scale for both... |
blob | commitdiff | diff to current |
2023-09-12 |
Ben Soares | JAL-4285 Better checkFiles processing. Better dialog. |
blob | commitdiff | diff to current |
2023-09-12 |
Ben Soares | JAL-4285 JAL-4262 Added a scrollable dialog to display... |
blob | commitdiff | diff to current |
2023-09-11 |
Ben Soares | Merge branch 'improvement/JAL-4262_deprecation_warning_... |
blob | commitdiff | diff to current |
2023-09-11 |
Ben Soares | JAL-4284 JAL-4285 Deal with output files/images consist... |
blob | commitdiff | diff to current |
2023-09-08 |
Ben Soares | JAL-4262 Dialog for GUI and WARN for CLI of old style... |
blob | commitdiff | diff to current |
2023-09-07 |
James Procter | JAL-4279 move on if the file doesn't exist, or Identify... |
blob | commitdiff | diff to current |
2023-09-07 |
James Procter | JAL-4279 catch exceptions with fileLoader and report... |
blob | commitdiff | diff to current |
2023-09-01 |
Ben Soares | Merge branch 'feature/JAL-629_--output_-_means_output_t... |
blob | commitdiff | diff to current |
2023-09-01 |
Ben Soares | JAL-629 Fix --structureimage and options |
blob | commitdiff | diff to current |
2023-08-31 |
Ben Soares | Merge branch 'features/r2_11_2_alphafold/JAL-629' into... |
blob | commitdiff | diff to current |
2023-08-31 |
Ben Soares | JAL-629 Small buglet with getting --seqid features/r2_11_2_alphafold/JAL-629 |
blob | commitdiff | diff to current |
2023-08-23 |
Ben Soares | Merge branch 'improvement/JAL-4250_secondary_structure_... |
blob | commitdiff | diff to current |
2023-08-23 |
Ben Soares | JAL-4250 Fix one word bug for 'af.createEPS(file, rende... |
blob | commitdiff | diff to current |
2023-08-18 |
Ben Soares | Merge branch 'feature/JAL-244_Automatically_adjust_left... |
blob | commitdiff | diff to current |
2023-08-09 |
Ben Soares | JAL-629 Move more stdout messages to stderr when output... |
blob | commitdiff | diff to current |
2023-08-09 |
Ben Soares | JAL-629 Default to FASTA if no format given for output... |
blob | commitdiff | diff to current |
2023-08-09 |
Ben Soares | JAL-629 Enable output to STDOUT when specifying output... |
blob | commitdiff | diff to current |
2023-08-02 |
Ben Soares | JAL-244 Fix buglet with automatic change in id column... |
blob | commitdiff | diff to current |
2023-08-01 |
Ben Soares | JAL-244 More control of automatic idWidth adjustments... |
blob | commitdiff | diff to current |
2023-07-27 |
Ben Soares | JAL-244 Allow adjusting Id column width in wrap mode... |
blob | commitdiff | diff to current |
2023-07-21 |
Ben Soares | JAL-244 Fixed idWidth labels in headless mode for non... |
blob | commitdiff | diff to current |
2023-07-07 |
James Procter | JAL-4217 JAL-629 built in 25s time out waiting for... |
blob | commitdiff | diff to current |
2023-07-07 |
James Procter | JAL-629 even more console debug for --structureviewer... |
blob | commitdiff | diff to current |
2023-07-06 |
James Procter | JAL-629 liberal defensive coding, comments about refact... |
blob | commitdiff | diff to current |
2023-07-06 |
James Procter | JAL-4217 interruptedExceptions should also break any... |
blob | commitdiff | diff to current |
2023-06-08 |
James Procter | JAL-4196 report an error if structure view doesn’t... |
blob | commitdiff | diff to current |
2023-06-07 |
James Procter | JAL-4195 add exception handling for all image output... |
blob | commitdiff | diff to current |
2023-06-07 |
James Procter | JAL-4195 catch thrown exceptions (if any) during image... |
blob | commitdiff | diff to current |
2023-06-06 |
James Procter | JAL-4160 --colour can now take user defined scheme... |
blob | commitdiff | diff to current |
2023-06-06 |
James Procter | JAL-4160 JAL-4195 wait around until alignFrame calculat... |
blob | commitdiff | diff to current |
2023-06-06 |
James Procter | JAL-4195 Debug message indicating creation of an image... |
blob | commitdiff | diff to current |
2023-06-01 |
Ben Soares | JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt... |
blob | commitdiff | diff to current |
2023-05-23 |
Ben Soares | JAL-629 Updated help docs and fixed structure image... |
blob | commitdiff | diff to current |
2023-05-23 |
Ben Soares | JAL-629 Added --structureimage code and formatting... |
blob | commitdiff | diff to current |
2023-05-22 |
Ben Soares | JAL-629 --structureimage with formatting args. |
blob | commitdiff | diff to current |
2023-05-18 |
Ben Soares | JAL-629 Added 'Type' to args and argvalues |
blob | commitdiff | diff to current |
2023-05-15 |
Ben Soares | Revert "JAL-629 Add a --threads argument to allow a... |
blob | commitdiff | diff to current |
2023-05-15 |
Ben Soares | JAL-629 Add a --threads argument to allow a limited... |
blob | commitdiff | diff to current |
2023-05-12 |
Ben Soares | JAL-629 Added --opened arg which is like limiting ... |
blob | commitdiff | diff to current |
2023-05-11 |
Ben Soares | JAL-629 Fix --tempfac. Hide non-working --notempfac... |
blob | commitdiff | diff to current |
2023-05-11 |
Ben Soares | JAL-629 Added linkedId to ArgValuesMap for reference... |
blob | commitdiff | diff to current |
2023-05-10 |
Ben Soares | JAL-629 More docs. Usage statement. Adjust some logging... |
blob | commitdiff | diff to current |
2023-05-09 |
Ben Soares | JAL-629 Add --seqid for non-subval use, make arg value... |
blob | commitdiff | diff to current |
2023-05-09 |
Ben Soares | JAL-629 change --renderer to --textrenderer to be more... |
blob | commitdiff | diff to current |
2023-05-04 |
Ben Soares | JAL-629 More NG arguments: --features, --annotations... |
blob | commitdiff | diff to current |
2023-05-03 |
Ben Soares | JAL-629 added eps and imagemap. Added --output and... |
blob | commitdiff | diff to current |
2023-05-02 |
Ben Soares | JAL-629 Changed --newframe and --allframes to --new... |
blob | commitdiff | diff to current |
2023-05-02 |
Ben Soares | JAL-629 Add --renderer arg/subval for vector output... |
blob | commitdiff | diff to current |
2023-04-30 |
Ben Soares | JAL-629 Change behaviour of --open GLOB to increment... |
blob | commitdiff | diff to current |
2023-04-28 |
Ben Soares | JAL-629 Change colour scheme shortnames to something... |
blob | commitdiff | diff to current |
2023-04-27 |
Ben Soares | JAL-629 Fixed appending URLs |
blob | commitdiff | diff to current |
2023-04-23 |
Ben Soares | JAL-629 Change --open to --append and --opennew to... |
blob | commitdiff | diff to current |
2023-04-22 |
Ben Soares | JAL-629 Test and fix --annotation --ssannotation args... |
blob | commitdiff | diff to current |
2023-04-19 |
Ben Soares | JAL-629 Now showing temp fac and secondary structure... |
blob | commitdiff | diff to current |
2023-04-14 |
Ben Soares | JAL-629 Adding PAE and TFType at structure loading... |
blob | commitdiff | diff to current |
2023-04-12 |
Ben Soares | JAL-629 parse SubVals once with ArgValue. Ensure SubVal... |
blob | commitdiff | diff to current |
2023-04-05 |
Ben Soares | JAL-629 Tests for FileUtils. Tidying counter substituti... |
blob | commitdiff | diff to current |
2023-04-04 |
Ben Soares | JAL-629 More consistent printing of --arguments. Exampl... |
blob | commitdiff | diff to current |
2023-03-29 |
Ben Soares | JAL-629 Added --opennew --nonews --nosplash. Added... |
blob | commitdiff | diff to current |
2023-03-28 |
Ben Soares | JAL-629 Opening files in new windows. not working yet |
blob | commitdiff | diff to current |
2023-03-25 |
Ben Soares | JAL-629 improvements to argparser toString. Improvement... |
blob | commitdiff | diff to current |
2023-03-23 |
Ben Soares | JAL-629 refactor ArgParser and helper classes all to... |
blob | commitdiff | diff to current |
2023-03-17 |
Ben Soares | JAL-629 All applications System.exits going through... |
blob | commitdiff | diff to current |
2023-03-15 |
Ben Soares | JAL-629 Commands more objecty, less classy. FileLoader... |
blob | commitdiff | diff to current |
2023-03-08 |
Ben Soares | JAL-629 --close individually for each AlignFrame opened... |
blob | commitdiff | diff to current |
2023-03-08 |
Ben Soares | JAL-629 Fix --headless for new args. Fix progressbar... |
blob | commitdiff | diff to current |
2023-03-03 |
Ben Soares | JAL-629 Improved consistency of ArgParser classes ... |
blob | commitdiff | diff to current |
2023-03-02 |
Ben Soares | JAL-629 Some refactoring to allow more flexible use... |
blob | commitdiff | diff to current |
2023-02-28 |
Ben Soares | JAL-629 Firm up bootstrapArgs. Correct '-colour' in... |
blob | commitdiff | diff to current |
2023-02-27 |
Ben Soares | JAL-629 Fix Exceptions when running with CLI not headless |
blob | commitdiff | diff to current |
2023-02-27 |
Ben Soares | JAL-629 removed debug prints. added .cif. added some... |
blob | commitdiff | diff to current |
2023-02-24 |
Ben Soares | JAL-629 Made ArgValuesMap helper class, simplifies... |
blob | commitdiff | diff to current |
2023-02-23 |
Ben Soares | JAL-629 bootstrap args and properties. Remember index... |
blob | commitdiff | diff to current |
2023-02-03 |
Ben Soares | JAL-629 Fasta sequence id reading whitespace fix. Flexi... |
blob | commitdiff | diff to current |
2023-01-26 |
Ben Soares | JAL-629 adjust arg type for tempfac-shading -- was... |
blob | commitdiff | diff to current |
2023-01-24 |
James Procter | JAL-629 hacked in --tempfac-shading - hardcoded to... |
blob | commitdiff | diff to current |
next |